Carbohydrate Binding Module Family 6

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• Author: ^^^Mirjam Czjzek^^^
• Responsible Curator: ^^^Mirjam Czjzek^^^

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CAZy DB link

https://www.cazy.org/CBM6.html

Ligand specificities

The ligand specificity of the first characterized CBM6, originating from a multimodular xylanase from Clostridium thermocellum, was determined to be xylan [1], although the results showed that this CBM6 was also able to bind to Avicel and acid-swollen cellulose. This was also the first CBM6 for which a 3D structure was determined [2], and multiple sequence alignments, analyzed in the light of this first 3D structure, already gave clear indications that large diversity in specificity was to be expected among CBM6 modules [2]. CBM6 modules are in general attached to bacterial, polysacchride degrading enzymes and can be found attached to xylanases, cellulases, agarases, laminarinases, etc [3]. Those having characterized binding activities cover both linear and branched/decorated xylan, β-1,4-glucan (or cellulose), mixed-linked β-1,3-1,4-glucan (or lichenan), agarose, β-1,3-glucan (or laminarin) and chitin. Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

Note: Here is an example of how to insert references in the text, together with the "biblio" section below: Please see these references for an essential introduction to the CAZy classification system: [4, 5]. CBMs, in particular, have been extensively reviewed [6, 7, 8, 9].

Structural Features

Content in this section should include, in paragraph form, a description of:

• Fold: Likewise many other CBMs, the overall fold corresponds to a β-sandwich, but the first identified ligand binding site was not, as usual, located at a shallow cleft on the concave surface of the β-sheets (cleft B in CBM6). Alternatively, a binding site was found located within the connecting loops of the two β-sheets (cleft A in CBM6). Interestingly, some CBM6s display binding affinities for both binding sites
• Type: Include here Type A, B, or C and properties
• Features of ligand binding: Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

Functionalities

Content in this section should include, in paragraph form, a description of:

• Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
• Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
• Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

Family Firsts

First Identified

Insert archetype here, possibly including very brief synopsis.

First Structural Characterization

Insert archetype here, possibly including very brief synopsis.

References

1. Fernandes AC, Fontes CM, Gilbert HJ, Hazlewood GP, Fernandes TH, and Ferreira LM. (1999). Homologous xylanases from Clostridium thermocellum: evidence for bi-functional activity, synergism between xylanase catalytic modules and the presence of xylan-binding domains in enzyme complexes. Biochem J. 1999;342 ( Pt 1)(Pt 1):105-10. | Google Books | Open Library
2. Czjzek M, Bolam DN, Mosbah A, Allouch J, Fontes CM, Ferreira LM, Bornet O, Zamboni V, Darbon H, Smith NL, Black GW, Henrissat B, and Gilbert HJ. (2001). The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. J Biol Chem. 2001;276(51):48580-7. DOI:10.1074/jbc.M109142200 |
3. Michel G, Barbeyron T, Kloareg B, and Czjzek M. (2009). The family 6 carbohydrate-binding modules have coevolved with their appended catalytic modules toward similar substrate specificity. Glycobiology. 2009;19(6):615-23. DOI:10.1093/glycob/cwp028 |
7. Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
8. Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
9. Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |